Variant simulator; report

Node used for reconstructing ancestral genome sequence

If a (newick) phylogenetic tree file has been provided, the visualisation of the MSA used in the calculations is shown below. The two chosen groups (i.e. ‘ingroup’ / species of interest, and outgroup) are highlighted in the tree. The outgroup, used in the computation or not, is the outgroup, which together with the reference species of interest coalesce at the node of interest, from which the ancestral sequence have been extracted. Most recent common ancestor (MRCA) is highlighted in purple and labeled. The rest of the clades in the alignment are shown in lighter grey. Regardless whether a reconstructed ancestral sequence at a node, or an outgroup, has been chosen as the ancestor, the MRCA will be highlighted.

Distribution of simulated variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of simulated variants is shown across the genome of the species of interest. The grey distribution corresponds to the total amount of simulated variants, whereas the red distribution corresponds to the subset that is overlapping with a corresponding non-gap ancestral sequence. If there is no forced sub-sampling due to lack of ancestral sequence, the distribution will be fully red.

Distribution of derived variants across the reference genome

If an ideogram (often possible to download on the UCSC website, here) has been provided, the distribution of derived variants is shown across the genome of the species of interest. The distribution of derived variants across the genome is shown in red.

How much of the reference genome that has an available, aligned reconstructed ancestral sequence

Table 1 Fraction of refence genome that has an available aligned reconstructed ancestral sequence. The leftmost column represents the total size of the source chromosome (in base pairs), from the species of interest. The middle column represents the size (in base pairs) of the recontructed ancestral genome (or size of aligned outgroup without gaps). The rightmost column represents the fraction of the reference genome that is covered by an ancestral sequence, i.e. the fraction of the reference with a corresponding non-gap ancestral alignment.
Size of ref. genome Size of reconstructed genome Fraction covered of ref. genome
1 274 330 532 86 159 508 0.31
2 151 935 994 42 079 399 0.28
3 132 848 913 38 941 004 0.29
4 130 910 915 35 125 192 0.27
5 104 526 007 28 152 729 0.27
6 170 843 587 49 771 406 0.29
7 121 844 099 36 176 581 0.30
8 138 966 237 39 184 925 0.28
9 139 512 083 39 347 045 0.28
10 69 359 453 18 023 566 0.26
11 79 169 978 20 562 672 0.26
12 61 602 749 17 125 428 0.28
13 208 334 590 58 674 576 0.28
14 141 755 446 38 729 099 0.27
15 140 412 725 43 101 389 0.31
16 79 944 280 25 502 491 0.32
17 63 494 081 8 217 468 0.13
18 55 982 971 16 738 833 0.30
X 125 939 595 23 370 700 0.19

Number of simulated variants

and how many are overlapping with an available ancestral sequence

Table with corresponding data:
Table 2.
Fraction of simulated SNPs that is overlapping with a reconstructed ancestral sequence. Column explanation from left to right:
i) chromosome number
ii) the total number of simulated SNPs
iii) the number of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
iv) the fraction of simulated SNPs that are overlapping with a non-gap align recontructed ancestral sequence.
v) the total number of derived variants.
No of sim. SNPs Number of sim. SNPs overlapping ancestral seq. Fraction of sim. SNPs overlapping ancestral seq. Number of derived variants
1 21 510 286 6 788 060 0.32 6 283 119
2 11 528 866 3 217 615 0.28 3 179 750
3 11 366 663 3 355 934 0.30 3 025 293
4 9 916 072 2 673 733 0.27 2 670 223
5 7 690 332 2 031 561 0.26 2 078 453
6 14 255 805 4 132 979 0.29 3 814 374
7 9 818 652 2 895 073 0.29 2 694 127
8 10 875 288 3 094 369 0.28 3 034 273
9 10 840 234 3 061 868 0.28 3 003 488
10 5 899 105 1 534 792 0.26 1 494 533
11 6 225 882 1 633 621 0.26 1 631 502
12 5 401 919 1 512 103 0.28 1 347 813
13 14 385 434 4 038 093 0.28 4 214 175
14 10 334 451 2 826 459 0.27 2 842 089
15 10 643 152 3 253 026 0.31 3 105 298
16 6 846 634 2 193 949 0.32 1 959 793
17 3 230 295 422 904 0.13 655 900
18 4 892 087 1 471 860 0.30 1 310 988
X 6 271 200 1 195 934 0.19 1 649 212

Types of simulated mutations

Table with corresponding data:
Table 3
Fraction of mutation types across the simulated variants with an available corresponding ancestral sequence. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions
v) the fraction of CpG site mutations
vi) the fraction of non-CpG mutations (transitions + transversions)
No. of SNPs Fraction transitions Fraction transversions Fraction CpGs Fraction non-CpGs (1-CpGs)
1 6 788 060 0.51 0.33 0.16 0.84
2 3 217 615 0.48 0.31 0.20 0.80
3 3 355 934 0.47 0.30 0.23 0.77
4 2 673 733 0.48 0.31 0.20 0.80
5 2 031 561 0.49 0.32 0.20 0.80
6 4 132 979 0.47 0.30 0.22 0.78
7 2 895 073 0.49 0.31 0.20 0.80
8 3 094 369 0.50 0.33 0.17 0.83
9 3 061 868 0.49 0.32 0.18 0.82
10 1 534 792 0.47 0.31 0.22 0.78
11 1 633 621 0.48 0.31 0.21 0.79
12 1 512 103 0.44 0.28 0.28 0.72
13 4 038 093 0.51 0.33 0.16 0.84
14 2 826 459 0.48 0.31 0.21 0.79
15 3 253 026 0.51 0.34 0.15 0.85
16 2 193 949 0.51 0.33 0.16 0.84
17 422 904 0.37 0.24 0.40 0.60
18 1 471 860 0.48 0.31 0.21 0.79
X 1 195 934 0.45 0.29 0.26 0.74

Types of derived mutations*

  • CpG mutation information is not available.

##### Table with corresponding data:

Table 4
Fraction of mutation types across the derived variants. Column explanation, starting from left:
i) chromosome number
ii) the total number of SNPs
iii) the fraction of transitions
iv) the fraction of transversions.
No. of SNPs Fraction transitions Fraction transversions
1 6 283 119 0.62 0.38
2 3 179 750 0.61 0.39
3 3 025 293 0.60 0.40
4 2 670 223 0.61 0.39
5 2 078 453 0.61 0.39
6 3 814 374 0.61 0.39
7 2 694 127 0.61 0.39
8 3 034 273 0.60 0.40
9 3 003 488 0.61 0.39
10 1 494 533 0.59 0.41
11 1 631 502 0.59 0.41
12 1 347 813 0.60 0.40
13 4 214 175 0.62 0.38
14 2 842 089 0.62 0.38
15 3 105 298 0.62 0.38
16 1 959 793 0.61 0.39
17 655 900 0.60 0.40
18 1 310 988 0.60 0.40
X 1 649 212 0.60 0.40

Visualisation of gene density

and CDS overlap

Validation of simulation parameters

Number of mutations, fractions, and substitution rates. To make sure the simulation was performed as expected, the leftmost part is the calculated numbers and rates in the parameter files, including the total number of simulated variants per chromosome, based on information from the ancestor and reference species. The middle part is the (re)calculated numbers and rates based on the total number of simulated variants. The rightmost part is the (re)calculated numbers and rates within the subset with a corresponding non-gap ancestral sequence. The comparison of parameters and simulated variants is to make sure that the simulation has been perform as intended, and the comparison between total set and the subset is to make sure that the distribution is the same even if the variants are forced to be down-sampled due to the lack of an available ancestral sequence.

Comparison of numebr of mutations between log files and actual simulated files
Parameter files
Simulated variant file
Simulated variant file
(filtered for positions with a corresponding non-gap ancestral position)
Chromosome considered: 1 Chromosome considered: 1 Chromosome considered: 1
Total mut: 7879034 Total mut: 18241993 Total mut: 5723919
#AC AG AT #AC AG AT #AC AG AT
559782 1326488 465209 1415055 3145270 1013054 441895 981463 315932
7.10% 16.84% 5.90% 7.76% 17.24% 5.55% 7.72% 17.15% 5.52%
#CA CG CT #CA CG CT #CA CG CT
271389 235588 1081570 589147 584580 2368592 186538 184877 746315
3.44% 2.99% 13.73% 3.23% 3.20% 12.98% 3.26% 3.23% 13.04%
#GA GC GT #GA GC GT #GA GC GT
1084226 237088 272652 2369651 585618 589252 747648 184885 186033
13.76% 3.01% 3.46% 12.99% 3.21% 3.23% 13.06% 3.23% 3.25%
#TA TC TG #TA TC TG #TA TC TG
463801 1323364 557877 1012740 3150041 1418993 317799 985766 444768
5.89% 16.80% 7.08% 5.55% 17.27% 7.78% 5.55% 17.22% 7.77%
Total CpG mut: 1066255 Total CpG mut: 3268293 Total CpG mut: 1064141
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
96180 85509 350937 285502 288606 1059920 92748 93908 345284
9.02% 8.02% 32.91% 8.74% 8.83% 32.43% 8.72% 8.82% 32.45%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
352231 85149 96249 1059355 289364 285546 344829 94187 93185
33.03% 7.99% 9.03% 32.41% 8.85% 8.74% 32.40% 8.85% 8.76%
Chromosome considered: 2 Chromosome considered: 2 Chromosome considered: 2
Total mut: 4021863 Total mut: 27486750 Total mut: 8282249
#AC AG AT #AC AG AT #AC AG AT
318655 696536 221949 2106723 4686746 1508923 634501 1409467 453678
7.92% 17.32% 5.52% 7.66% 17.05% 5.49% 7.66% 17.02% 5.48%
#CA CG CT #CA CG CT #CA CG CT
125726 132775 514926 903296 895678 3633160 273515 270952 1095330
3.13% 3.30% 12.80% 3.29% 3.26% 13.22% 3.30% 3.27% 13.23%
#GA GC GT #GA GC GT #GA GC GT
514853 133106 126015 3633930 897510 904127 1096529 271048 273196
12.80% 3.31% 3.13% 13.22% 3.27% 3.29% 13.24% 3.27% 3.30%
#TA TC TG #TA TC TG #TA TC TG
221827 697274 318221 1508036 4694796 2113825 454799 1412899 636335
5.52% 17.34% 7.91% 5.49% 17.08% 7.69% 5.49% 17.06% 7.68%
Total CpG mut: 555669 Total CpG mut: 5552402 Total CpG mut: 1723426
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
47607 50332 179905 485016 490497 1800399 150906 152169 558604
8.57% 9.06% 32.38% 8.74% 8.83% 32.43% 8.76% 8.83% 32.41%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
179784 49993 48048 1800318 490841 485331 558589 152290 150868
32.35% 9.00% 8.65% 32.42% 8.84% 8.74% 32.41% 8.84% 8.75%
Chromosome considered: 3 Chromosome considered: 3 Chromosome considered: 3
Total mut: 3870463 Total mut: 36330228 Total mut: 10874867
#AC AG AT #AC AG AT #AC AG AT
329154 690957 205326 2755594 6125743 1972990 823420 1828281 589316
8.50% 17.85% 5.30% 7.58% 16.86% 5.43% 7.57% 16.81% 5.42%
#CA CG CT #CA CG CT #CA CG CT
113139 131648 465450 1213301 1204821 4883861 365426 362122 1463872
2.92% 3.40% 12.03% 3.34% 3.32% 13.44% 3.36% 3.33% 13.46%
#GA GC GT #GA GC GT #GA GC GT
465545 131770 114196 4884914 1205389 1215532 1465436 362146 365600
12.03% 3.40% 2.95% 13.45% 3.32% 3.35% 13.48% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
204783 687951 330544 1971198 6135010 2761875 589974 1833161 826113
5.29% 17.77% 8.54% 5.43% 16.89% 7.60% 5.43% 16.86% 7.60%
Total CpG mut: 562265 Total CpG mut: 8075587 Total CpG mut: 2486742
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
47196 56034 177562 706154 713360 2617588 217826 219541 805923
8.39% 9.97% 31.58% 8.74% 8.83% 32.41% 8.76% 8.83% 32.41%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
178078 56358 47037 2619289 713020 706176 806667 219302 217483
31.67% 10.02% 8.37% 32.43% 8.83% 8.74% 32.44% 8.82% 8.75%
Chromosome considered: 4 Chromosome considered: 4 Chromosome considered: 4
Total mut: 3455992 Total mut: 44277261 Total mut: 13006074
#AC AG AT #AC AG AT #AC AG AT
283985 627002 193190 3359781 7471313 2405424 985286 2186919 704535
8.22% 18.14% 5.59% 7.59% 16.87% 5.43% 7.58% 16.81% 5.42%
#CA CG CT #CA CG CT #CA CG CT
101776 105657 414289 1477078 1466150 5947006 436710 432704 1750150
2.94% 3.06% 11.99% 3.34% 3.31% 13.43% 3.36% 3.33% 13.46%
#GA GC GT #GA GC GT #GA GC GT
416867 106236 103546 5950010 1468405 1479711 1752776 433055 436629
12.06% 3.07% 3.00% 13.44% 3.32% 3.34% 13.48% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
192708 625969 284767 2403629 7480069 3368685 705604 2193546 988160
5.58% 18.11% 8.24% 5.43% 16.89% 7.61% 5.43% 16.87% 7.60%
Total CpG mut: 409496 Total CpG mut: 10044626 Total CpG mut: 3029268
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
35999 36896 131130 878568 887408 3255734 265255 267542 981557
8.79% 9.01% 32.02% 8.75% 8.83% 32.41% 8.76% 8.83% 32.40%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
131517 37336 36618 3258286 886691 877939 983176 267024 264714
32.12% 9.12% 8.94% 32.44% 8.83% 8.74% 32.46% 8.81% 8.74%
Chromosome considered: 5 Chromosome considered: 5 Chromosome considered: 5
Total mut: 2637688 Total mut: 50322436 Total mut: 14640050
#AC AG AT #AC AG AT #AC AG AT
212345 470633 148095 3814510 8485158 2730190 1109424 2463636 793687
8.05% 17.84% 5.61% 7.58% 16.86% 5.43% 7.58% 16.83% 5.42%
#CA CG CT #CA CG CT #CA CG CT
79256 79673 327175 1680368 1668912 6767747 490558 486183 1967373
3.00% 3.02% 12.40% 3.34% 3.32% 13.45% 3.35% 3.32% 13.44%
#GA GC GT #GA GC GT #GA GC GT
328743 79730 79903 6770280 1672162 1683734 1969716 486825 490961
12.46% 3.02% 3.03% 13.45% 3.32% 3.35% 13.45% 3.33% 3.35%
#TA TC TG #TA TC TG #TA TC TG
148001 471072 213062 2729134 8495752 3824489 795063 2473309 1113315
5.61% 17.86% 8.08% 5.42% 16.88% 7.60% 5.43% 16.89% 7.60%
Total CpG mut: 311167 Total CpG mut: 11689783 Total CpG mut: 3426853
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
27286 27318 100461 1022299 1032948 3788738 299794 302882 1110625
8.77% 8.78% 32.29% 8.75% 8.84% 32.41% 8.75% 8.84% 32.41%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
101387 27279 27436 3792127 1032022 1021649 1112285 301978 299289
32.58% 8.77% 8.82% 32.44% 8.83% 8.74% 32.46% 8.81% 8.73%
Chromosome considered: 6 Chromosome considered: 6 Chromosome considered: 6
Total mut: 4827635 Total mut: 61333204 Total mut: 17846185
#AC AG AT #AC AG AT #AC AG AT
404441 862641 250671 4613767 10262837 3302120 1343215 2983127 960830
8.38% 17.87% 5.19% 7.52% 16.73% 5.38% 7.53% 16.72% 5.38%
#CA CG CT #CA CG CT #CA CG CT
140650 165018 592460 2071370 2058142 8346641 604110 599422 2425695
2.91% 3.42% 12.27% 3.38% 3.36% 13.61% 3.39% 3.36% 13.59%
#GA GC GT #GA GC GT #GA GC GT
590965 164846 140627 8346752 2061349 2075862 2426556 599660 604571
12.24% 3.41% 2.91% 13.61% 3.36% 3.38% 13.60% 3.36% 3.39%
#TA TC TG #TA TC TG #TA TC TG
251549 859889 403878 3299149 10270912 4624303 961399 2991415 1346185
5.21% 17.81% 8.37% 5.38% 16.75% 7.54% 5.39% 16.76% 7.54%
Total CpG mut: 706945 Total CpG mut: 14934820 Total CpG mut: 4353697
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
58010 68154 226831 1305458 1319783 4841023 380897 384817 1410992
8.21% 9.64% 32.09% 8.74% 8.84% 32.41% 8.75% 8.84% 32.41%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
227858 68467 57625 4844836 1318412 1305308 1412491 384055 380445
32.23% 9.68% 8.15% 32.44% 8.83% 8.74% 32.44% 8.82% 8.74%
Chromosome considered: 7 Chromosome considered: 7 Chromosome considered: 7
Total mut: 3405147 Total mut: 69145535 Total mut: 20167210
#AC AG AT #AC AG AT #AC AG AT
272776 595228 187528 5195705 11554513 3717476 1516308 3367540 1084636
8.01% 17.48% 5.51% 7.51% 16.71% 5.38% 7.52% 16.70% 5.38%
#CA CG CT #CA CG CT #CA CG CT
103797 107226 435248 2339281 2325307 9429141 683853 678314 2747014
3.05% 3.15% 12.78% 3.38% 3.36% 13.64% 3.39% 3.36% 13.62%
#GA GC GT #GA GC GT #GA GC GT
436620 107900 104449 9429456 2328732 2345235 2746284 678815 683920
12.82% 3.17% 3.07% 13.64% 3.37% 3.39% 13.62% 3.37% 3.39%
#TA TC TG #TA TC TG #TA TC TG
187370 593590 273415 3714293 11561160 5205236 1085653 3375279 1519594
5.50% 17.43% 8.03% 5.37% 16.72% 7.53% 5.38% 16.74% 7.53%
Total CpG mut: 468319 Total CpG mut: 16941141 Total CpG mut: 4927745
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
39552 40969 152921 1480869 1498058 5490923 431356 435935 1596513
8.45% 8.75% 32.65% 8.74% 8.84% 32.41% 8.75% 8.85% 32.40%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
153910 41125 39842 5495765 1494636 1480890 1598730 434389 430822
32.86% 8.78% 8.51% 32.44% 8.82% 8.74% 32.44% 8.82% 8.74%
Chromosome considered: 8 Chromosome considered: 8 Chromosome considered: 8
Total mut: 3926442 Total mut: 78209177 Total mut: 22720087
#AC AG AT #AC AG AT #AC AG AT
318657 705847 232189 5905733 13135520 4224774 1715232 3810696 1227073
8.12% 17.98% 5.91% 7.55% 16.80% 5.40% 7.55% 16.77% 5.40%
#CA CG CT #CA CG CT #CA CG CT
120111 114596 473112 2626585 2611449 10588448 765469 759467 3075852
3.06% 2.92% 12.05% 3.36% 3.34% 13.54% 3.37% 3.34% 13.54%
#GA GC GT #GA GC GT #GA GC GT
471492 114138 120157 10585266 2613994 2633261 3074546 759592 765699
12.01% 2.91% 3.06% 13.53% 3.34% 3.37% 13.53% 3.34% 3.37%
#TA TC TG #TA TC TG #TA TC TG
231973 705878 318292 4222098 13143113 5918936 1228207 3818323 1719931
5.91% 17.98% 8.11% 5.40% 16.81% 7.57% 5.41% 16.81% 7.57%
Total CpG mut: 427367 Total CpG mut: 18752787 Total CpG mut: 5469237
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
39006 37484 136784 1639482 1657366 6079401 478493 483400 1772873
9.13% 8.77% 32.01% 8.74% 8.84% 32.42% 8.75% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
137321 37865 38907 6082666 1654137 1639735 1773731 482144 478596
32.13% 8.86% 9.10% 32.44% 8.82% 8.74% 32.43% 8.82% 8.75%
Chromosome considered: 9 Chromosome considered: 9 Chromosome considered: 9
Total mut: 3848436 Total mut: 87078379 Total mut: 25219435
#AC AG AT #AC AG AT #AC AG AT
307690 683745 217520 6583130 14639649 4708308 1906154 4234910 1363396
8.00% 17.77% 5.65% 7.56% 16.81% 5.41% 7.56% 16.79% 5.41%
#CA CG CT #CA CG CT #CA CG CT
116822 118462 481527 2918891 2902504 11768114 847726 841705 3409435
3.04% 3.08% 12.51% 3.35% 3.33% 13.51% 3.36% 3.34% 13.52%
#GA GC GT #GA GC GT #GA GC GT
482625 118777 118178 11766242 2905798 2926811 3407863 842237 848459
12.54% 3.09% 3.07% 13.51% 3.34% 3.36% 13.51% 3.34% 3.36%
#TA TC TG #TA TC TG #TA TC TG
216223 679008 307859 4707330 14653919 6597683 1364592 4242642 1910316
5.62% 17.64% 8.00% 5.41% 16.83% 7.58% 5.41% 16.82% 7.57%
Total CpG mut: 462691 Total CpG mut: 20723819 Total CpG mut: 6031757
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
40375 40149 150760 1811547 1830887 6719598 527564 532887 1955552
8.73% 8.68% 32.58% 8.74% 8.83% 32.42% 8.75% 8.83% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
151491 39612 40304 6721544 1827962 1812281 1956010 532073 527671
32.74% 8.56% 8.71% 32.43% 8.82% 8.74% 32.43% 8.82% 8.75%
Chromosome considered: 10 Chromosome considered: 10 Chromosome considered: 10
Total mut: 2007270 Total mut: 91669387 Total mut: 26415704
#AC AG AT #AC AG AT #AC AG AT
192769 381338 108548 6927735 15405377 4954652 1996298 4434681 1427591
9.60% 19.00% 5.41% 7.56% 16.81% 5.40% 7.56% 16.79% 5.40%
#CA CG CT #CA CG CT #CA CG CT
52240 64176 207959 3074820 3057143 12396678 888214 881850 3572657
2.60% 3.20% 10.36% 3.35% 3.33% 13.52% 3.36% 3.34% 13.52%
#GA GC GT #GA GC GT #GA GC GT
206965 64023 52433 12392578 3060059 3083159 3571230 882370 888881
10.31% 3.19% 2.61% 13.52% 3.34% 3.36% 13.52% 3.34% 3.36%
#TA TC TG #TA TC TG #TA TC TG
107973 377562 191284 4953176 15420392 6943618 1428662 4442582 2000688
5.38% 18.81% 9.53% 5.40% 16.82% 7.57% 5.41% 16.82% 7.57%
Total CpG mut: 220782 Total CpG mut: 22031916 Total CpG mut: 6370280
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
18953 22460 68997 1925971 1946513 7143211 557091 562889 2065080
8.58% 10.17% 31.25% 8.74% 8.83% 32.42% 8.75% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
68628 22747 18997 7145802 1943544 1926875 2065746 562158 557316
31.08% 10.30% 8.60% 32.43% 8.82% 8.75% 32.43% 8.82% 8.75%
Chromosome considered: 11 Chromosome considered: 11 Chromosome considered: 11
Total mut: 2153486 Total mut: 96614464 Total mut: 27698768
#AC AG AT #AC AG AT #AC AG AT
189532 400992 120353 7311371 16256385 5228552 2095201 4653696 1498277
8.80% 18.62% 5.59% 7.57% 16.83% 5.41% 7.56% 16.80% 5.41%
#CA CG CT #CA CG CT #CA CG CT
62203 66498 236012 3234102 3216201 13038645 929894 923559 3741455
2.89% 3.09% 10.96% 3.35% 3.33% 13.50% 3.36% 3.33% 13.51%
#GA GC GT #GA GC GT #GA GC GT
235600 66499 62136 13033689 3218063 3242624 3740161 924222 930859
10.94% 3.09% 2.89% 13.49% 3.33% 3.36% 13.50% 3.34% 3.36%
#TA TC TG #TA TC TG #TA TC TG
121913 401390 190358 5228376 16276936 7329520 1499638 4662179 2099627
5.66% 18.64% 8.84% 5.41% 16.85% 7.59% 5.41% 16.83% 7.58%
Total CpG mut: 235853 Total CpG mut: 23312721 Total CpG mut: 6720837
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21321 22933 73551 2037367 2059810 7559601 587349 593926 2179260
9.04% 9.72% 31.19% 8.74% 8.84% 32.43% 8.74% 8.84% 32.43%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
73477 23077 21494 7561294 2056134 2038515 2179670 592714 587918
31.15% 9.78% 9.11% 32.43% 8.82% 8.74% 32.43% 8.82% 8.75%
Chromosome considered: 12 Chromosome considered: 12 Chromosome considered: 12
Total mut: 1739223 Total mut: 100536259 Total mut: 28783748
#AC AG AT #AC AG AT #AC AG AT
162561 330682 82188 7584009 16861675 5422703 2169874 4819179 1551559
9.35% 19.01% 4.73% 7.54% 16.77% 5.39% 7.54% 16.74% 5.39%
#CA CG CT #CA CG CT #CA CG CT
43808 65696 185857 3381557 3362709 13630284 971196 964390 3907168
2.52% 3.78% 10.69% 3.36% 3.34% 13.56% 3.37% 3.35% 13.57%
#GA GC GT #GA GC GT #GA GC GT
186531 66044 44288 13626567 3365138 3389630 3905894 965260 971997
10.72% 3.80% 2.55% 13.55% 3.35% 3.37% 13.57% 3.35% 3.38%
#TA TC TG #TA TC TG #TA TC TG
81908 328009 161651 5423795 16885014 7603178 1553474 4829174 2174583
4.71% 18.86% 9.29% 5.39% 16.79% 7.56% 5.40% 16.78% 7.55%
Total CpG mut: 266258 Total CpG mut: 24792845 Total CpG mut: 7147960
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21126 30191 81546 2166756 2191180 8038252 624633 631957 2317361
7.93% 11.34% 30.63% 8.74% 8.84% 32.42% 8.74% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
81686 30519 21190 8040568 2187058 2169031 2318033 630407 625569
30.68% 11.46% 7.96% 32.43% 8.82% 8.75% 32.43% 8.82% 8.75%
Chromosome considered: 13 Chromosome considered: 13 Chromosome considered: 13
Total mut: 5219361 Total mut: 112636880 Total mut: 32191211
#AC AG AT #AC AG AT #AC AG AT
337832 844280 317910 8524380 18952710 6095105 2434665 5407268 1741796
6.47% 16.18% 6.09% 7.57% 16.83% 5.41% 7.56% 16.80% 5.41%
#CA CG CT #CA CG CT #CA CG CT
194200 152150 763483 3770055 3747910 15192737 1080979 1072531 4348510
3.72% 2.92% 14.63% 3.35% 3.33% 13.49% 3.36% 3.33% 13.51%
#GA GC GT #GA GC GT #GA GC GT
764677 152584 194594 15187522 3751669 3780453 4346106 1074372 1082463
14.65% 2.92% 3.73% 13.48% 3.33% 3.36% 13.50% 3.34% 3.36%
#TA TC TG #TA TC TG #TA TC TG
317947 842301 337403 6100435 18985658 8548246 1742817 5419787 2439917
6.09% 16.14% 6.46% 5.42% 16.86% 7.59% 5.41% 16.84% 7.58%
Total CpG mut: 715184 Total CpG mut: 27077658 Total CpG mut: 7778590
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
65708 51890 239364 2366801 2393269 8779163 679729 687940 2521586
9.19% 7.26% 33.47% 8.74% 8.84% 32.42% 8.74% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
240675 51779 65768 8781131 2388193 2369101 2522395 686046 680894
33.65% 7.24% 9.20% 32.43% 8.82% 8.75% 32.43% 8.82% 8.75%
Chromosome considered: 14 Chromosome considered: 14 Chromosome considered: 14
Total mut: 3551055 Total mut: 120816720 Total mut: 34425985
#AC AG AT #AC AG AT #AC AG AT
270257 609183 195748 9129624 20297570 6528054 2600586 5774279 1860540
7.61% 17.15% 5.51% 7.56% 16.80% 5.40% 7.55% 16.77% 5.40%
#CA CG CT #CA CG CT #CA CG CT
112860 112977 473442 4052524 4028202 16333096 1158185 1148743 4660308
3.18% 3.18% 13.33% 3.35% 3.33% 13.52% 3.36% 3.34% 13.54%
#GA GC GT #GA GC GT #GA GC GT
475948 113436 114301 16327383 4032976 4064095 4657910 1150879 1159883
13.40% 3.19% 3.22% 13.51% 3.34% 3.36% 13.53% 3.34% 3.37%
#TA TC TG #TA TC TG #TA TC TG
194648 607393 270862 6534519 20334239 9154438 1860877 5788414 2605381
5.48% 17.10% 7.63% 5.41% 16.83% 7.58% 5.41% 16.81% 7.57%
Total CpG mut: 553296 Total CpG mut: 29232269 Total CpG mut: 8370275
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
46113 46383 183977 2555556 2583259 9477923 731105 740308 2713517
8.33% 8.38% 33.25% 8.74% 8.84% 32.42% 8.73% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
183477 46460 46886 9478871 2578705 2557955 2714220 738357 732768
33.16% 8.40% 8.47% 32.43% 8.82% 8.75% 32.43% 8.82% 8.75%
Chromosome considered: 15 Chromosome considered: 15 Chromosome considered: 15
Total mut: 3893223 Total mut: 129831654 Total mut: 37191953
#AC AG AT #AC AG AT #AC AG AT
272023 657621 236596 9831872 21860221 7030289 2817506 6256372 2015539
6.99% 16.89% 6.08% 7.57% 16.84% 5.41% 7.58% 16.82% 5.42%
#CA CG CT #CA CG CT #CA CG CT
136355 110753 532286 4340467 4315146 17493352 1246230 1236162 5014705
3.50% 2.84% 13.67% 3.34% 3.32% 13.47% 3.35% 3.32% 13.48%
#GA GC GT #GA GC GT #GA GC GT
532083 110997 135302 17488195 4319664 4352679 5012873 1237952 1247961
13.67% 2.85% 3.48% 13.47% 3.33% 3.35% 13.48% 3.33% 3.36%
#TA TC TG #TA TC TG #TA TC TG
236189 659741 273277 7038556 21902337 9858876 2015407 6269405 2821841
6.07% 16.95% 7.02% 5.42% 16.87% 7.59% 5.42% 16.86% 7.59%
Total CpG mut: 495293 Total CpG mut: 30860487 Total CpG mut: 8857333
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
46081 38407 163353 2698002 2726915 10005507 773716 783373 2871565
9.30% 7.75% 32.98% 8.74% 8.84% 32.42% 8.74% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
162612 38760 46080 10006328 2722554 2701181 2871897 781194 775588
32.83% 7.83% 9.30% 32.42% 8.82% 8.75% 32.42% 8.82% 8.76%
Chromosome considered: 16 Chromosome considered: 16 Chromosome considered: 16
Total mut: 2504364 Total mut: 135620253 Total mut: 39035659
#AC AG AT #AC AG AT #AC AG AT
188337 423451 146848 10283297 22862823 7353090 2960267 6573631 2117459
7.52% 16.91% 5.86% 7.58% 16.86% 5.42% 7.58% 16.84% 5.42%
#CA CG CT #CA CG CT #CA CG CT
84179 76680 329108 4527798 4500820 18246671 1306437 1296023 5257521
3.36% 3.06% 13.14% 3.34% 3.32% 13.45% 3.35% 3.32% 13.47%
#GA GC GT #GA GC GT #GA GC GT
327309 76303 83099 18238619 4504300 4539530 5255094 1297529 1308030
13.07% 3.05% 3.32% 13.45% 3.32% 3.35% 13.46% 3.32% 3.35%
#TA TC TG #TA TC TG #TA TC TG
147937 432905 188208 7359265 22897664 10306376 2116581 6583714 2963373
5.91% 17.29% 7.52% 5.43% 16.88% 7.60% 5.42% 16.87% 7.59%
Total CpG mut: 318115 Total CpG mut: 31918522 Total CpG mut: 9207576
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
29140 26734 103892 2790890 2820460 10348256 804319 814469 2985145
9.16% 8.40% 32.66% 8.74% 8.84% 32.42% 8.74% 8.85% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
102833 26976 28540 10349173 2815745 2793998 2985245 812000 806398
32.33% 8.48% 8.97% 32.42% 8.82% 8.75% 32.42% 8.82% 8.76%
Chromosome considered: 17 Chromosome considered: 17 Chromosome considered: 17
Total mut: 855886 Total mut: 137574078 Total mut: 39289791
#AC AG AT #AC AG AT #AC AG AT
68251 152958 47240 10424509 23177402 7454110 2978760 6615153 2130709
7.97% 17.87% 5.52% 7.58% 16.85% 5.42% 7.58% 16.84% 5.42%
#CA CG CT #CA CG CT #CA CG CT
27900 29935 101717 4597100 4569888 18527341 1315269 1304972 5293654
3.26% 3.50% 11.88% 3.34% 3.32% 13.47% 3.35% 3.32% 13.47%
#GA GC GT #GA GC GT #GA GC GT
102177 29965 28091 18518665 4573214 4608886 5291102 1306424 1316970
11.94% 3.50% 3.28% 13.46% 3.32% 3.35% 13.47% 3.33% 3.35%
#TA TC TG #TA TC TG #TA TC TG
47006 152281 68365 7460786 23212960 10449217 2129854 6624726 2982198
5.49% 17.79% 7.99% 5.42% 16.87% 7.60% 5.42% 16.86% 7.59%
Total CpG mut: 129274 Total CpG mut: 33194992 Total CpG mut: 9376348
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
11310 13402 39828 2902309 2932978 10762240 818931 829252 3039873
8.75% 10.37% 30.81% 8.74% 8.84% 32.42% 8.73% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
39858 13308 11568 10763075 2928516 2905874 3040258 826831 821203
30.83% 10.29% 8.95% 32.42% 8.82% 8.75% 32.42% 8.82% 8.76%
Chromosome considered: 18 Chromosome considered: 18 Chromosome considered: 18
Total mut: 1693572 Total mut: 141445727 Total mut: 40445336
#AC AG AT #AC AG AT #AC AG AT
153394 319422 85873 10713235 23821773 7661062 3064451 6806486 2192356
9.06% 18.86% 5.07% 7.57% 16.84% 5.42% 7.58% 16.83% 5.42%
#CA CG CT #CA CG CT #CA CG CT
43881 54040 187718 4729810 4701941 19060477 1355223 1344242 5453512
2.59% 3.19% 11.08% 3.34% 3.32% 13.48% 3.35% 3.32% 13.48%
#GA GC GT #GA GC GT #GA GC GT
187536 54512 43632 19050206 4705117 4741551 5451360 1345767 1356855
11.07% 3.22% 2.58% 13.47% 3.33% 3.35% 13.48% 3.33% 3.35%
#TA TC TG #TA TC TG #TA TC TG
86173 323017 154374 7667303 23854713 10738539 2191228 6815869 3067987
5.09% 19.07% 9.12% 5.42% 16.86% 7.59% 5.42% 16.85% 7.59%
Total CpG mut: 204722 Total CpG mut: 34215430 Total CpG mut: 9692663
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
16989 20833 64639 2991755 3023169 11093387 846647 857396 3142666
8.30% 10.18% 31.57% 8.74% 8.84% 32.42% 8.73% 8.85% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
64842 20538 16881 11093588 3018785 2994746 3142267 854865 848822
31.67% 10.03% 8.25% 32.42% 8.82% 8.75% 32.42% 8.82% 8.76%
Chromosome considered: X Chromosome considered: X Chromosome considered: X
Total mut: 2078494 Total mut: 146234637 Total mut: 41331642
#AC AG AT #AC AG AT #AC AG AT
167172 359589 115834 11083903 24648243 7926148 3132381 6957803 2241156
8.04% 17.30% 5.57% 7.58% 16.86% 5.42% 7.58% 16.83% 5.42%
#CA CG CT #CA CG CT #CA CG CT
70863 65779 259447 4884615 4855232 19684144 1383915 1372850 5570450
3.41% 3.16% 12.48% 3.34% 3.32% 13.46% 3.35% 3.32% 13.48%
#GA GC GT #GA GC GT #GA GC GT
260215 66119 71005 19672985 4859210 4896635 5568047 1374881 1386024
12.52% 3.18% 3.42% 13.45% 3.32% 3.35% 13.47% 3.33% 3.35%
#TA TC TG #TA TC TG #TA TC TG
116755 358343 167373 7933123 24681005 11109394 2239959 6968104 3136072
5.62% 17.24% 8.05% 5.42% 16.88% 7.60% 5.42% 16.86% 7.59%
Total CpG mut: 234913 Total CpG mut: 35697720 Total CpG mut: 10002291
#CA CG CT (CpG) #CA CG CT (CpG) #CA CG CT (CpG)
21327 20018 76030 3121115 3153919 11574524 873551 884671 3243191
9.08% 8.52% 32.37% 8.74% 8.84% 32.42% 8.73% 8.84% 32.42%
#GA GC GT (CpG) #GA GC GT (CpG) #GA GC GT (CpG)
76092 19936 21510 11573705 3150198 3124259 3242650 882419 875809
32.39% 8.49% 9.16% 32.42% 8.82% 8.75% 32.42% 8.82% 8.76%